[This is part of a series on the tools I used to write my PhD. Check out the other parts here.]
My PhD included references to 479 individual sources. It's well known that formatting issues often plague students just prior to submission of their dissertations. A reference manager can help solve most of these problems.
When I began my PhD, I was using Sente, a Mac-only programme, but towards the end I transitioned to Bookends. There's no particular reason for the change, mainly that Bookends is a slightly sparer-design.
Different journals and universities require different formatting of references and sources. Bookends (or whatever you choose) is an easy way to stay on top of these formatting issues.
It connects easily (via a shortcut) to Scrivener or many other word processing tools that are commonly used. If you have many references like me, you can colour code them to make it easy to see what's what at a glance (see the image above for part of the database I used for my PhD).
I don't, however, use Bookends as a repository for PDFs and documents. You can do this, technically, but it's not ideal. You're far better off keeping your reference manage for what it does well, and then having a separate file system for your PDFs and other documents (like DevonThink, for example).